[1] Rephrased extensively, the stanza would probably mean "Though it is but wishful thinking, my desire to someday understand (the meaning of) that [something] which lies between successive periods of darkness." A possible interpretation would be that the persona seeks to see the sky in daylight for herself, something which she is unable to do.

[2] What this stanza likely refers to is that despite the persona's desire to simply disappear (die) in peace (while still having hope of being rescued), and despite being exhausted from evading a person who seeks to kill her, she is still waiting [for something].

[3] This song contains much imagery which is not only difficult (if not impossible) to translate, but also rather incomprehensible in the literal sense when read in the original Japanese. When appreciating the song, it might be helpful to consider it from the viewpoint of the character (Matsuri), who is practically an immortal [albeit one to whom exposure to sunlight is fatal] character haunted by sad memories of the past.